No problem, we understand. I would however recommend keeping in mind that there is still the possibility that a user error is the cause of all this. Which could mean that you will run into the same problem/outcome when using
SendModelingCommand, depending on what you are doing exactly.
The problem for me is still that I am not sure what you are doing exactly. E.g., what is the 'spiral modifier (data structure)' for you? But when I do what seems likely to be what you are doing, add a 'Twist Object' to some parametric spline input, 'Make Editable' works fine for me, both invoked from the app as well as a Python
It might be helpful to point out that there is a difference between 'Make Editable' and 'Current State to Object'. While the former will effectively replace a generator with its collapsed cache (not deform cache), the latter will collapse whole hierarchies and also include deform caches in this collapsing. Depending on what you are doing, this will make a huge difference, especially when you start copying things, as nodes collapsed with 'Make Editable' still have dependencies. I.e., when you copy the output of 'Make Editable' without its children, tags, etc. just somewhere else, it could very well be that this copied object then is missing other things which influence it in some way, resulting for example in your odd outputs.
Me poking around with a simple example: